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install_unix.md

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Building ngs-bits from sources (Linux/MacOS)

Dependencies

ngs-bits depends on the following software to be installed

  • g++ (4.5 or higher)
  • qmake (Qt 5.9 or higher, including xmlpatterns and mysql package)
  • git (to extract the version hash)
  • optional: python and matplotlib (for plot generation in QC tools)

For example, the installation of the dependencies using Ubuntu 16.04/18.04 looks like that:

> sudo apt-get install git make g++ qt5-default libqt5xmlpatterns5-dev libqt5sql5-mysql git python python-matplotlib libbz2-dev liblzma-dev libcurl4 libcurl4-openssl-dev

Download

Use git to clone the most recent release (the source code package of GitHub does not contains required sub-modules):

> git clone --recursive https://github.com/imgag/ngs-bits.git
> cd ngs-bits
> git checkout 2021_06
> git submodule update --recursive --init

Resolving proxy issues with git

If you are behind a proxy that blocks the standard git port, you see something like this:

> git clone --recursive https://github.com/imgag/ngs-bits.git
Cloning into 'ngs-bits'...
fatal: Unable to look up github.com (port 9418) (Name or service not known)

Then you have to adapt your ~/.gitconfig file like that:

[http]
proxy = http://[user]:[password]@[host]:[port]

Build

Just execute the following make commands:

> make build_3rdparty
> make build_libs_release
> make build_tools_release

Executing

Now the executables and all required libraries can be found in the bin folder.

Setting the reference genome

Some of the ngs-bits tools need a reference genome in FASTA format.
You can set the reference genome on the command line, e.g. the -ref parameter of the VcfLeftNormalize tool.

To avoid having to set the reference genome for each call, you can set up a settings file.
Copy the template:

> cp bin/settings.ini.example bin/settings.ini

and then set the reference_genome parameter in the bin/settings.ini file.

Setting up the NGSD (optional)

Some of the tools need the NGSD, a MySQL database that contains for example gene, transcript and exon data.
Installation instructions for the NGSD can be found here.

Building GSvar (optional)

GSvar is a GUI for viewing the variant calls produced by the megSAP pipeline.
Additionally, it offers a user interface to the NGSD (see above).

To build GSvar, execute the following command:

> make build_gui_release

Now you need to configure GSVar.